BN1749 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 2.5469e-06 2.4447e-04
Layer 4 5.4215e-06 2.1522e-05
Layer 5 7.7252e-06 7.2836e-05
Layer 6 2.0331e-05 1.1536e-03
Layer 2 1.5932e-03 2.4534e-02
WM 9.9999e-01 7.6526e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
NDRG4 Expression Distribution
Gene Specificity Score (GSS)
NDRG4 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
NDRG4 Layer 5 3.3711 0.9190
ATP1A3 Layer 5 3.3438 0.9181
SERPINI1 Layer 4 3.5742 0.9174
SYP Layer 5 3.4160 0.9160
ATP1A1 Layer 5 3.3496 0.9153
GTF2I Layer 4 3.3145 0.9152
EIF4G2 Layer 5 3.2930 0.9142
SPTAN1 Layer 4 3.3945 0.9134
PRKACB Layer 5 3.1738 0.9127
FAIM2 Layer 5 3.2637 0.9127
YPEL3 Layer 5 3.4160 0.9124
NAP1L1 Layer 4 3.1387 0.9123
PRKAR1B Layer 5 3.2012 0.9119
GDI1 Layer 5 3.3496 0.9118
PPP2R1A Layer 5 3.1191 0.9118
ATP2A2 Layer 4 3.3574 0.9116
MEF2C Layer 4 3.5664 0.9115
STMN3 Layer 5 3.3398 0.9114
DDX24 Layer 4 3.1875 0.9114
RNF11 Layer 5 3.0254 0.9111
PLD3 Layer 5 3.3496 0.9111
TAGLN3 Layer 5 3.1562 0.9108
PJA2 Layer 4 3.2363 0.9107
NPTN Layer 4 3.3828 0.9106
CACYBP Layer 5 3.2256 0.9102
MGST3 Layer 5 3.3438 0.9100
KLC1 Layer 4 3.2852 0.9092
FKBP8 Layer 5 3.2227 0.9091
TMOD2 Layer 5 3.3145 0.9090
NDFIP1 Layer 5 3.3789 0.9090
MYL6 Layer 5 3.2363 0.9089
LGALS1 Layer 5 3.4375 0.9085
ALDOC Layer 5 3.2793 0.9085
PREPL Layer 4 3.3223 0.9085
REEP5 Layer 4 3.4531 0.9084
CELF4 Layer 4 3.4453 0.9081
ATP6V1B2 Layer 5 3.2852 0.9080
PI4KA Layer 5 3.1904 0.9079
ISCU Layer 5 3.2188 0.9077
MORF4L2 Layer 4 3.2012 0.9070
ENO2 Layer 4 3.3438 0.9070
RAC1 Layer 5 3.0586 0.9068
MDH1 Layer 5 3.3359 0.9068
SNX3 Layer 5 3.0859 0.9066
SH3GL2 Layer 4 3.3613 0.9066
BSCL2 Layer 5 3.1191 0.9065
MYO5A Layer 4 3.3145 0.9061
HSP90B1 Layer 5 2.9697 0.9058
SEPTIN7 Layer 4 3.0283 0.9058
PFKP Layer 5 3.3359 0.9057

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1749
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1749_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1749/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1749/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1749/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1749/report/PD/BN1749_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1749/report/PD/BN1749_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 06:45:06
  • Number of Processes: 10
  • Spending Time: 0h 4m